Question: ChAMP champ.norm BMIQ produces differing results
0
gravatar for Gurkenkönig
3 months ago by
Gurkenkönig0 wrote:

The method produces different results with each run. Can anyone give me a hint on how to fix this behavior?

set.seed(42)
library("ChAMP")
myLoad_test1 <- champ.load(directory = "data/raw/iDat_t0",
           method="ChAMP",
           methValue="B",
           autoimpute=TRUE,
           filterDetP=TRUE,
           ProbeCutoff=0,
           SampleCutoff=0.1,
           detPcut=0.01,
           filterBeads=TRUE,
           beadCutoff=0.05,
           filterNoCG=TRUE,
           filterSNPs=TRUE,
           population=NULL,
           filterMultiHit=TRUE,
           filterXY=TRUE,
           force=FALSE,
           arraytype="EPIC")

gc()
myNorm_test_1.1 <- champ.norm(beta=myLoad_test1$beta,
               rgSet=myLoad_test1$rgSet,
               mset=myLoad_test1$mset,
               resultsDir="./CHAMP_Normalization/",
               method="BMIQ",
               plotBMIQ=FALSE,
               arraytype="EPIC",
               cores=1)

gc()
myNorm_test_1.2 <- champ.norm(beta=myLoad_test1$beta,
               rgSet=myLoad_test1$rgSet,
               mset=myLoad_test1$mset,
               resultsDir="./CHAMP_Normalization/",
               method="BMIQ",
               plotBMIQ=FALSE,
               arraytype="EPIC",
               cores=1)

print(identical(myNorm_test_1.1, myNorm_test_1.2))
myNorm_test_1.1[1:5,1:5]
myNorm_test_1.2[1:5,1:5]


[1] FALSE
              SPL-066    SPL-005    SPL-001    SPL-013    SPL-021
cg07881041 0.96269795 0.93971660 0.96005661 0.96662973 0.94678340
cg03513874 0.96182761 0.96468813 0.96690889 0.96146023 0.95427445
cg05451842 0.02726911 0.03012527 0.03381639 0.02627537 0.02072133
cg14797042 0.97285162 0.98219496 0.97348613 0.96923460 0.98554301
cg09838562 0.02913757 0.02983066 0.03453992 0.04064944 0.02684536
              SPL-066    SPL-005    SPL-001    SPL-013    SPL-021
cg07881041 0.96152149 0.94004936 0.96097521 0.96574810 0.94501442
cg03513874 0.96063812 0.96527364 0.96765142 0.96053807 0.95271938
cg05451842 0.02757454 0.02976092 0.03170889 0.03010782 0.01929390
cg14797042 0.97184842 0.98277645 0.97406201 0.96837768 0.98495060
cg09838562 0.02944406 0.02948598 0.03235829 0.05618163 0.02507286


> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
 [1] splines   stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ChAMP_2.12.4                               IlluminaHumanMethylationEPICmanifest_0.3.0
 [3] Illumina450ProbeVariants.db_1.18.0         DMRcate_1.18.0                            
 [5] DMRcatedata_1.18.0                         DSS_2.30.1                                
 [7] bsseq_1.18.0                               FEM_3.10.0                                
 [9] graph_1.60.0                               org.Hs.eg.db_3.7.0                        
[11] impute_1.56.0                              igraph_1.2.4                              
[13] corrplot_0.84                              marray_1.60.0                             
[15] limma_3.38.3                               Matrix_1.2-14                             
[17] AnnotationDbi_1.44.0                       ChAMPdata_2.14.1                          
[19] minfi_1.28.3                               bumphunter_1.24.5                         
[21] locfit_1.5-9.1                             iterators_1.0.10                          
[23] foreach_1.4.4                              Biostrings_2.50.2                         
[25] XVector_0.22.0                             SummarizedExperiment_1.12.0               
[27] DelayedArray_0.8.0                         BiocParallel_1.16.6                       
[29] matrixStats_0.54.0                         Biobase_2.42.0                            
[31] GenomicRanges_1.34.0                       GenomeInfoDb_1.18.2                       
[33] IRanges_2.16.0                             S4Vectors_0.20.1                          
[35] BiocGenerics_0.28.0                        RevoUtils_11.0.1                          
[37] RevoUtilsMath_11.0.0                      

loaded via a namespace (and not attached):
  [1] rtracklayer_1.42.1                                  prabclus_2.2-7                                     
  [3] R.methodsS3_1.7.1                                   wateRmelon_1.26.0                                  
  [5] pkgmaker_0.27                                       tidyr_0.8.2                                        
  [7] ggplot2_3.1.0                                       acepack_1.4.1                                      
  [9] bit64_0.9-7                                         knitr_1.21                                         
 [11] R.utils_2.8.0                                       data.table_1.12.0                                  
 [13] rpart_4.1-13                                        RCurl_1.95-4.11                                    
 [15] GEOquery_2.50.5                                     AnnotationFilter_1.6.0                             
 [17] doParallel_1.0.14                                   GenomicFeatures_1.34.3                             
 [19] preprocessCore_1.44.0                               RSQLite_2.1.1                                      
 [21] combinat_0.0-8                                      bit_1.1-14                                         
 [23] xml2_1.2.0                                          httpuv_1.4.5.1                                     
 [25] assertthat_0.2.0                                    IlluminaHumanMethylation450kmanifest_0.4.0         
 [27] viridis_0.5.1                                       IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
 [29] isva_1.9                                            xfun_0.5                                           
 [31] hms_0.4.2                                           evaluate_0.13                                      
 [33] missMethyl_1.16.0                                   DNAcopy_1.56.0                                     
 [35] promises_1.0.1                                      DEoptimR_1.0-8                                     
 [37] progress_1.2.0                                      dendextend_1.9.0                                   
 [39] DBI_1.0.0                                           htmlwidgets_1.3                                    
 [41] reshape_0.8.8                                       purrr_0.3.0                                        
 [43] ROC_1.58.0                                          dplyr_0.7.6                                        
 [45] backports_1.1.3                                     trimcluster_0.1-2.1                                
 [47] permute_0.9-4                                       annotate_1.60.0                                    
 [49] biomaRt_2.38.0                                      ensembldb_2.6.6                                    
 [51] withr_2.1.2                                         globaltest_5.36.0                                  
 [53] Gviz_1.26.5                                         robustbase_0.93-3                                  
 [55] BSgenome_1.50.0                                     checkmate_1.9.1                                    
 [57] GenomicAlignments_1.18.1                            prettyunits_1.0.2                                  
 [59] mclust_5.4.2                                        cluster_2.0.7-1                                    
 [61] RPMM_1.25                                           lazyeval_0.2.1                                     
 [63] crayon_1.3.4                                        genefilter_1.64.0                                  
 [65] pkgconfig_2.0.2                                     nlme_3.1-137                                       
 [67] ProtGenerics_1.14.0                                 nnet_7.3-12                                        
 [69] bindr_0.1.1                                         rlang_0.3.1                                        
 [71] diptest_0.75-7                                      nleqslv_3.3.2                                      
 [73] registry_0.5                                        affyio_1.52.0                                      
 [75] dichromat_2.0-0                                     rngtools_1.3.1                                     
 [77] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  base64_2.0                                         
 [79] Rhdf5lib_1.4.2                                      base64enc_0.1-3                                    
 [81] geneLenDataBase_1.18.0                              whisker_0.3-2                                      
 [83] viridisLite_0.3.0                                   bitops_1.0-6                                       
 [85] R.oo_1.22.0                                         KernSmooth_2.23-15                                 
 [87] blob_1.1.1                                          DelayedMatrixStats_1.4.0                           
 [89] doRNG_1.7.1                                         stringr_1.4.0                                      
 [91] qvalue_2.14.1                                       nor1mix_1.2-3                                      
 [93] readr_1.3.1                                         scales_1.0.0                                       
 [95] memoise_1.1.0                                       magrittr_1.5                                       
 [97] plyr_1.8.4                                          bibtex_0.4.2                                       
 [99] zlibbioc_1.28.0                                     compiler_3.5.1                                     
[101] RColorBrewer_1.1-2                                  illuminaio_0.24.0                                  
[103] clue_0.3-56                                         Rsamtools_1.34.1                                   
[105] affy_1.60.0                                         JADE_2.0-1                                         
[107] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 htmlTable_1.13.1                                   
[109] Formula_1.2-3                                       MASS_7.3-50                                        
[111] mgcv_1.8-24                                         tidyselect_0.2.5                                   
[113] stringi_1.1.7                                       yaml_2.2.0                                         
[115] askpass_1.1                                         latticeExtra_0.6-28                                
[117] grid_3.5.1                                          VariantAnnotation_1.28.11                          
[119] tools_3.5.1                                         ruv_0.9.7                                          
[121] rstudioapi_0.9.0                                    foreign_0.8-70                                     
[123] gridExtra_2.3                                       digest_0.6.18                                      
[125] BiocManager_1.30.4                                  shiny_1.2.0                                        
[127] quadprog_1.5-5                                      fpc_2.1-11.1                                       
[129] bindrcpp_0.2.2                                      Rcpp_1.0.0                                         
[131] siggenes_1.56.0                                     later_0.8.0                                        
[133] httr_1.4.0                                          biovizBase_1.30.1                                  
[135] lumi_2.34.0                                         kernlab_0.9-27                                     
[137] colorspace_1.4-0                                    XML_3.98-1.17                                      
[139] statmod_1.4.30                                      kpmt_0.1.0                                         
[141] multtest_2.38.0                                     shinythemes_1.1.2                                  
[143] flexmix_2.3-15                                      plotly_4.8.0                                       
[145] xtable_1.8-3                                        jsonlite_1.6                                       
[147] modeltools_0.2-22                                   R6_2.4.0                                           
[149] Hmisc_4.2-0                                         pillar_1.3.1                                       
[151] htmltools_0.3.6                                     mime_0.6                                           
[153] glue_1.3.0                                          class_7.3-14                                       
[155] beanplot_1.2                                        codetools_0.2-16                                   
[157] mvtnorm_1.0-8                                       lattice_0.20-35                                    
[159] tibble_2.0.1                                        sva_3.30.1                                         
[161] curl_3.3                                            BiasedUrn_1.07                                     
[163] gtools_3.8.1                                        GO.db_3.7.0                                        
[165] openssl_1.2.1                                       survival_2.42-3                                    
[167] rmarkdown_1.11                                      methylumi_2.28.0                                   
[169] fastICA_1.2-1                                       munsell_0.5.0                                      
[171] rhdf5_2.26.2                                        GenomeInfoDbData_1.2.0                             
[173] goseq_1.34.1                                        HDF5Array_1.10.1                                   
[175] reshape2_1.4.3                                      gtable_0.2.0
microarray normalization • 109 views
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